[R] OrgMassSpecR peak area issue

[Bryan Hanson]

If you type DrawChromatogram you can see the method used to calculate the peak area.  Looks to me like you could easily hack it if you wanted.  The relevant part about peak areas is this:

        for (j in 1:n) {
            k <- (j%%n) + 1
            x[j] <- peakTime[j] * peakIntensity[k] - peakTime[k] * 
                peakIntensity[j]
        }
        peakArea[i] <- abs(sum(x)/2)

which looks pretty standard to me, though I'm not clear right off the top of my head why they are dividing by 2.  You can always contact the maintainer.

Bryan

On Mar 18, 2013, at 1:34 PM, Christopher Beaver <christopher.beaver at gmail.com> wrote:

> Hello!
> 
> I am having an issue with the OrgMassSpecR package.  I run my HPLC using a
> DAD detector.  My raw data is exported form chemstation as a csv file.  I
> then upload the csv into Rstudio no problem.  Using the DrawChromatogram
> function, I get a nice chromatogram, and my retention time, peak area, and
> apex intensity values are given as well.
> 
> The problem comes with the peak area value given. The peak area is much
> smaller than a value that would make sense.  My peak area value is actually
> less than my apex intensity value.  Is this because I am using a DAD
> detector rather than an MS? If so, is there a simply way to edit the peak
> area equation so that it will also work with absorbance values?
> 
> Any help is greatly appreciated.
> 
> Thanks for your time.
> 
> Chris Beaver
> 
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> 
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